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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ), 'gf_id' => 'HOM05D001193', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001193' ), 'data_identifier' => 'HOM05D001193', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001193', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p05870' => 'bna', 'A05p17620' => 'bna', 'A05p25260' => 'bna', 'A08p00790' => 'bna', 'A08p03930' => 'bna', 'Aa31LG10G4530' => 'aar', 'Aa31LG11G6890' => 'aar', 'Aa31LG2G13870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.4111' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.445' => 'aag', 'Actinidia04634' => 'ach', 'Actinidia06855' => 'ach', 'Actinidia12965' => 'ach', 'Actinidia14752' => 'ach', 'Actinidia16267' => 'ach', 'Actinidia16268' => 'ach', 'Actinidia18151' => 'ach', 'Ah.01g019880' => 'amhyb', 'Ah.06g193050' => 'amhyb', 'Ah.07g201210' => 'amhyb', 'Ah.10g033400' => 'amhyb', 'Ah.12g055900' => 'amhyb', 'AL1G46200' => 'aly', 'AL1G56790' => 'aly', 'AL1G63270' => 'aly', 'AL1G63280' => 'aly', 'AL6G31400' => 'aly', 'Aqoxy5G03031' => 'aox', 'Aqoxy7G00856' => 'aox', 'Aqoxy7G01067' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0E5TT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UZ95K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFX8YV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5PPYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZF9QJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PM0FQ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q3NKK5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5VF9E' => 'arhy', 'AT1G32127' => 'ath', 'AT1G49470' => 'ath', 'AT1G55230' => 'ath', 'AT1G55240' => 'ath', 'AT5G19870' => 'ath', 'ATR0598G107' => 'atr', 'ATR0598G351' => 'atr', 'ATR0829G135' => 'atr', 'Atru.chr13.1399' => 'acertr', 'Atru.chr3.2251' => 'acertr', 'Atru.chr3.2252' => 'acertr', 'Atru.chr5.2874' => 'acertr', 'Atru.chr6.1502' => 'acertr', 'AUR62000028' => 'cqu', 'AUR62000029' => 'cqu', 'AUR62007396' => 'cqu', 'AUR62011399' => 'cqu', 'AUR62016659' => 'cqu', 'AUR62019199' => 'cqu', 'AUR62027334' => 'cqu', 'BcaB02g10838' => 'bca', 'BcaB03g13763' => 'bca', 'BcaB04g16971' => 'bca', 'BcaB04g16974' => 'bca', 'BcaB04g17337' => 'bca', 'BcaB07g32874' => 'bca', 'BcaB07g32877' => 'bca', 'BcaC01g01479' => 'bca', 'BcaC01g01500' => 'bca', 'BcaC01g01506' => 'bca', 'BcaC03g13720' => 'bca', 'BcaC05g27238' => 'bca', 'BcaC05g27240' => 'bca', 'BcaC05g27925' => 'bca', 'BcaC07g37049' => 'bca', 'BcaC08g44183' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p02030' => 'bna', 'BolC2t06989H' => 'bol', 'BolC3t21559H' => 'bol', 'BolC3t21560H' => 'bol', 'BolC3t21564H' => 'bol', 'BolC3t21567H' => 'bol', 'BolC3t21568H' => 'bol', 'BolC5t32667H' => 'bol', 'BolC6t36778H' => 'bol', 'BolC8t47218H' => 'bol', 'BraA02t05539Z' => 'bra', 'BraA05t20653Z' => 'bra', 'BraA05t21402Z' => 'bra', 'BraA08t32136Z' => 'bra', 'BraA08t32139Z' => 'bra', 'BraA08t32422Z' => 'bra', 'C03p92480' => 'bna', 'C03p92490' => 'bna', 'C03p92540' => 'bna', 'C05p39310' => 'bna', 'C06p15870' => 'bna', 'C08p04160' => 'bna', 'CAN.G1269.6' => 'can', 'CAN.G1269.8' => 'can', 'CAN.G140.52' => 'can', 'CAN.G158.1' => 'can', 'CAN.G917.3' => 'can', 'CANSAT11G0788' => 'cansat', 'CANSAT11G0819' => 'cansat', 'CANSAT25G0687' => 'cansat', 'CARHR031470' => 'chi', 'CARHR031480' => 'chi', 'CARHR039470' => 'chi', 'CARHR044880' => 'chi', 'CARHR044890' => 'chi', 'CARHR123320' => 'chi', 'CARHR123330' => 'chi', 'CARHR193010' => 'chi', 'Carub.0001s3044' => 'cru', 'Carub.0001s3865' => 'cru', 'Carub.0006s1823' => 'cru', 'Ca_20816_v3' => 'car', 'Ca_22487_v3' => 'car', 'Ca_25114_v3' => 'car', 'Cc01_g01530' => 'ccan', 'Cc01_g01560' => 'ccan', 'Cc01_g01570' => 'ccan', 'Cc01_g01620' => 'ccan', 'Cc02_g18200' => 'ccan', 'Cc08_g04370' => 'ccan', 'Cc08_g05670' => 'ccan', 'Cc09_g09630' => 'ccan', 'CDE01G0295' => 'cde', 'CDE05G2126' => 'cde', 'CDE05G2215' => 'cde', 'Cfa004945' => 'cfa', 'Cfa009613' => 'cfa', 'Cfa012578' => 'cfa', 'Ciclev10002116m.g' => 'ccl', 'Ciclev10016008m.g' => 'ccl', 'Ciclev10017774m.g' => 'ccl', 'Ciclev10018173m.g' => 'ccl', 'Ciclev10028950m.g' => 'ccl', 'CiPaw.05G058600' => 'cil', 'CiPaw.11G102200' => 'cil', 'CiPaw.12G071000' => 'cil', 'CiPaw.13G172500' => 'cil', 'CiPaw.13G172700' => 'cil', 'CiPaw.13G172900' => 'cil', 'CiPaw.14G133700' => 'cil', 'CiPaw.14G133800' => 'cil', 'CiPaw.14G133900' => 'cil', 'ClCG02G005530' => 'cla', 'ClCG02G023880' => 'cla', 'ClCG10G001100' => 'cla', 'COL.COLO4_16872' => 'col', 'COL.COLO4_17773' => 'col', 'COL.COLO4_27475' => 'col', 'COL.COLO4_34986' => 'col', 'COL.COLO4_34987' => 'col', 'Cpa.g.sc119.84' => 'cpa', 'Cpa.g.sc119.85' => 'cpa', 'Cpa.g.sc24.59' => 'cpa', 'Cpa.g.sc62.79' => 'cpa', 'Cre06.g283900' => 'cre', 'Cre06.g299350' => 'cre', 'CsaV3_3G001120' => 'csa', 'CsaV3_4G023470' => 'csa', 'CsaV3_7G010100' => 'csa', 'CSS0001070' => 'camsi', 'CSS0013003' => 'camsi', 'CSS0018231' => 'camsi', 'CSS0042143' => 'camsi', 'CSS0046353' => 'camsi', 'DCAR_004249' => 'dca', 'DCAR_015034' => 'dca', 'DCAR_017676' => 'dca', 'DCAR_025420' => 'dca', 'DCAR_028244' => 'dca', 'DCAR_029009' => 'dca', 'Dinv13425' => 'din', 'Dinv22847' => 'din', 'Dinv23579' => 'din', 'Dinv28030' => 'din', 'Dinv29058' => 'din', 'Duzib052G0027' => 'dzi', 'Duzib068G0065' => 'dzi', 'Duzib132G0105' => 'dzi', 'Duzib150G1262' => 'dzi', 'Duzib168G1939' => 'dzi', 'Duzib168G2045' => 'dzi', 'Duzib170G0809' => 'dzi', 'ECA236G2558' => 'eca', 'ECA246G0418' => 'eca', 'ECA246G1774' => 'eca', 'EL10Ac2g03533' => 'bvu', 'EL10Ac4g10349' => 'bvu', 'EL10Ac5g11949' => 'bvu', 'EL10Ac9g21793' => 'bvu', 'Eucgr.B03626' => 'egr', 'Eucgr.D02606' => 'egr', 'Eucgr.F03330' => 'egr', 'Eucgr.G00509' => 'egr', 'Eucgr.G01533' => 'egr', 'Eucgr.J01790' => 'egr', 'FAN03G1463' => 'fan', 'FAN04G2489' => 'fan', 'FAN06G0354' => 'fan', 'FAN08G0973' => 'fan', 'FAN10G0052' => 'fan', 'FAN11G3039' => 'fan', 'FAN13G2524' => 'fan', 'FAN15G2329' => 'fan', 'FAN16G0935' => 'fan', 'FAN18G3519' => 'fan', 'FAN18G4260' => 'fan', 'FAN20G3093' => 'fan', 'FAN21G3972' => 'fan', 'FAN24G2224' => 'fan', 'FAN25G1836' => 'fan', 'FvH4_2g07340' => 'fve', 'FvH4_3g44810' => 'fve', 'FvH4_5g23820' => 'fve', 'FvH4_7g04431' => 'fve', 'Glyma.01G148300' => 'gma', 'Glyma.03G021300' => 'gma', 'Glyma.07G256300' => 'gma', 'Glyma.07G256400' => 'gma', 'Glyma.09G212200' => 'gma', 'Glyma.10G279200' => 'gma', 'Glyma.11G123900' => 'gma', 'Glyma.12G048400' => 'gma', 'Glyma.13G209600' => 'gma', 'Glyma.15G103000' => 'gma', 'Glyma.16G104000' => 'gma', 'Glyma.20G110500' => 'gma', 'Gohir.A03G214400' => 'ghi', 'Gohir.A08G011800' => 'ghi', 'Gohir.A08G079400' => 'ghi', 'Gohir.A08G150900' => 'ghi', 'Gohir.D02G235900' => 'ghi', 'Gohir.D08G022300' => 'ghi', 'Gohir.D08G088900' => 'ghi', 'Gohir.D08G172000' => 'ghi', 'Gorai.004G017600' => 'gra', 'Gorai.004G093600' => 'gra', 'Gorai.004G179300' => 'gra', 'Gorai.005G264000' => 'gra', 'GSVIVG01022610001' => 'vvi', 'GSVIVG01031878001' => 'vvi', 'GSVIVG01036879001' => 'vvi', 'HanXRQChr02g0056601' => 'han', 'HanXRQChr06g0172841' => 'han', 'HanXRQChr16g0506061' => 'han', 'HanXRQChr17g0537371' => 'han', 'Haze_08081' => 'cav', 'Haze_08084' => 'cav', 'Hma1.2p1_0075F.1_g039160' => 'hma', 'Hma1.2p1_1179F.1_g264500' => 'hma', 'HPP92_001469' => 'vpl', 'HPP92_001481' => 'vpl', 'HPP92_016186' => 'vpl', 'HPP92_026731' => 'vpl', 'HPP92_028613' => 'vpl', 'HPP92_028614' => 'vpl', 'HPP92_028664' => 'vpl', 'HPP92_028665' => 'vpl', 'Hund14338' => 'sun', 'Lalb_Chr05g0215501' => 'lal', 'Lalb_Chr15g0087341' => 'lal', 'Lalb_Chr16g0380831' => 'lal', 'Lalb_Chr18g0056051' => 'lal', 'Lalb_Chr19g0138501' => 'lal', 'Lalb_Chr21g0309201' => 'lal', 'Lj1g0000881' => 'lja', 'Lj1P548T12' => 'lonja', 'Lj1P549T4' => 'lonja', 'Lj1P550T26' => 'lonja', 'Lj1P551T7' => 'lonja', 'Lj1P552T4' => 'lonja', 'Lj2g0013531' => 'lja', 'Lj3g0025270' => 'lja', 'Lj4g0010733' => 'lja', 'Lj4g0028217' => 'lja', 'Lj5g0005816' => 'lja', 'Lj5P203T41' => 'lonja', 'Lj6g0005093' => 'lja', 'Lj7C161T7' => 'lonja', 'Lsat_1_v5_gn_3_20520' => 'lsa', 'Lsat_1_v5_gn_6_51800' => 'lsa', 'Lsat_1_v5_gn_6_51820' => 'lsa', 'Lsat_1_v5_gn_6_51840' => 'lsa', 'Lsat_1_v5_gn_6_52561' => 'lsa', 'Lsat_1_v5_gn_7_88001' => 'lsa', 'Manes.03G088500' => 'mes', 'Manes.03G088503' => 'mes', 'Manes.03G088519' => 'mes', 'Manes.15G105200' => 'mes', 'Manes.15G105400' => 'mes', 'Manes.15G145500' => 'mes', 'Manes.17G008600' => 'mes', 'Mapoly0016s0059' => 'mpo', 'Mapoly0090s0038' => 'mpo', 'Mapoly0093s0064' => 'mpo', 'MBI13_g29635_MAGBIO' => 'mbi', 'MBI19_g17434_MAGBIO' => 'mbi', 'MD00G1000700' => 'mdo', 'MD03G1010300' => 'mdo', 'MD03G1010400' => 'mdo', 'MD05G1072300' => 'mdo', 'MD06G1014200' => 'mdo', 'MD11G1012300' => 'mdo', 'Medtr1g112150' => 'mtr', 'Medtr1g112160' => 'mtr', 'Medtr2g021690' => 'mtr', 'Medtr4g068340' => 'mtr', 'Medtr5g027180' => 'mtr', 'Medtr8g071140' => 'mtr', 'Medtr8g071150' => 'mtr', 'MELO3C013802.2' => 'cme', 'MELO3C014669.2' => 'cme', 'Migut.D02534' => 'egut', 'Migut.E01340' => 'egut', 'Migut.N01211' => 'egut', 'Migut.N01805' => 'egut', 'MSTRG.13977' => 'ama', 'MSTRG.1779' => 'ama', 'MSTRG.18859' => 'ama', 'MSTRG.28047' => 'ama', 'Nitab4.5_0000488g0030' => 'nta', 'Nitab4.5_0001033g0030' => 'nta', 'Nitab4.5_0002543g0010' => 'nta', 'Nitab4.5_0002733g0050' => 'nta', 'Nitab4.5_0005466g0020' => 'nta', 'Nitab4.5_0009295g0020' => 'nta', 'Nn1g07157' => 'nnu', 'Nn1g08906' => 'nnu', 'Nn2g10767' => 'nnu', 'Nn2g15762' => 'nnu', 'Nn2g15763' => 'nnu', 'Nn3g21170' => 'nnu', 'Nn4g23863' => 'nnu', 'Nn7g35937' => 'nnu', 'Nn8g39284' => 'nnu', 'Oeu003706.1' => 'oeu', 'Oeu010569.1' => 'oeu', 'Oeu027364.1' => 'oeu', 'Oeu030969.1' => 'oeu', 'Oeu031899.1' => 'oeu', 'Oeu038586.1' => 'oeu', 'Oeu046519.1' => 'oeu', 'Oeu061085.1' => 'oeu', 'Os08g0462800' => 'osa', 'Os08g0462900' => 'osa', 'Os09g0444800' => 'osa', 'Os09g0444900' => 'osa', 'Os11g0621000' => 'osa', 'Peaxi162Scf00003g02218' => 'pax', 'Peaxi162Scf00100g00063' => 'pax', 'Peaxi162Scf00100g00091' => 'pax', 'Peaxi162Scf00100g00410' => 'pax', 'Peaxi162Scf00100g00512' => 'pax', 'Peaxi162Scf00100g00513' => 'pax', 'Peaxi162Scf00408g00069' => 'pax', 'Peaxi162Scf78515g00001' => 'pax', 'PGR031G0267' => 'pgr', 'PGR042G2327' => 'pgr', 'PGR102G0601' => 'pgr', 'PGR102G1186' => 'pgr', 'PGR119G2075' => 'pgr', 'PGSC0003DMG400006222' => 'stu', 'PGSC0003DMG400018930' => 'stu', 'PGSC0003DMG400030882' => 'stu', 'PGSC0003DMG400032228' => 'stu', 'Phvul.001G085900' => 'pvu', 'Phvul.002G131900' => 'pvu', 'Phvul.003G095000' => 'pvu', 'Phvul.003G272800' => 'pvu', 'Phvul.006G154700' => 'pvu', 'Phvul.007G022100' => 'pvu', 'Potri.001G008900' => 'ptr', 'Potri.001G009000' => 'ptr', 'Potri.001G132800' => 'ptr', 'Potri.003G100700' => 'ptr', 'Potri.003G216500' => 'ptr', 'Potri.003G216600' => 'ptr', 'Potri.009G108900' => 'ptr', 'Pp3c1_25080' => 'ppa', 'Pp3c26_500' => 'ppa', 'Pp3c5_8910' => 'ppa', 'PRCOL_00004731' => 'pco', 'Prupe.5G022200' => 'ppe', 'Prupe.6G010200' => 'ppe', 'Prupe.8G112800' => 'ppe', 'Psat1g184320' => 'psa', 'Psat2g141400' => 'psa', 'Psat4g110560' => 'psa', 'Psat6g230800' => 'psa', 'Psat6g230840' => 'psa', 'Psat7g208040' => 'psa', 'PSO017G4028' => 'pso', 'PSO135G0199' => 'pso', 'PSO339G4892' => 'pso', 'PSO384G3666' => 'pso', 'PSO384G4910' => 'pso', 'PSO541G5489' => 'pso', 'QL01p010431' => 'qlo', 'QL11p039205' => 'qlo', 'QL12p000927' => 'qlo', 'QL12p000933' => 'qlo', 'RcHm_v2.0_Chr2g0124381' => 'rch', 'RcHm_v2.0_Chr5g0081481' => 'rch', 'RcHm_v2.0_Chr6g0260051' => 'rch', 'RcHm_v2.0_Chr6g0260061' => 'rch', 'RcHm_v2.0_Chr6g0260131' => 'rch', 'RcHm_v2.0_Chr6g0260141' => 'rch', 'RcHm_v2.0_Chr6g0260341' => 'rch', 'RcHm_v2.0_Chr6g0260351' => 'rch', 'RcHm_v2.0_Chr6g0260371' => 'rch', 'RcHm_v2.0_Chr6g0260381' => 'rch', 'RcHm_v2.0_Chr6g0260551' => 'rch', 'RcHm_v2.0_Chr6g0260561' => 'rch', 'RcHm_v2.0_Chr6g0260601' => 'rch', 'RcHm_v2.0_Chr6g0260651' => 'rch', 'RcHm_v2.0_Chr6g0260741' => 'rch', 'RcHm_v2.0_Chr6g0260751' => 'rch', 'RcHm_v2.0_Chr7g0213211' => 'rch', 'Rhsim07G0137400' => 'rsi', 'Rhsim11G0026800' => 'rsi', 'Rhsim11G0170800' => 'rsi', 'Rhsim13G0229600' => 'rsi', 'Sabra01G0006900' => 'sbr', 'Sabra01G0102400' => 'sbr', 'Sabra03G0161500' => 'sbr', 'Sabra03G0161600' => 'sbr', 'Sabra03G0161700' => 'sbr', 'Sabra09G0083200' => 'sbr', 'SalBow3G3241' => 'sbo', 'SalBow4G2675' => 'sbo', 'SalBow6G1026' => 'sbo', 'SalBow6G2810' => 'sbo', 'SalBow6G3837' => 'sbo', 'SalBow6G5739' => 'sbo', 'SalBow6G6108' => 'sbo', 'Sc06g0004310' => 'sci', 'Sc09g0006600' => 'sci', 'Sc16g0012040' => 'sci', 'Sc22g0001980' => 'sci', 'Sed0001720' => 'sed', 'Sed0025947' => 'sed', 'Sed0025953' => 'sed', 'SEGI_08849' => 'sgi', 'SEGI_09378' => 'sgi', 'SEGI_20451' => 'sgi', 'SEGI_32026' => 'sgi', 'SEGI_32401' => 'sgi', 'SGA_v2.0_scaffold111G31372' => 'sas', 'SGA_v2.0_scaffold144G35873' => 'sas', 'SGA_v2.0_scaffold55G19827' => 'sas', 'SGA_v2.0_scaffold5G02945' => 'sas', 'SGA_v2.0_scaffold6G03447' => 'sas', 'SHI30458' => 'shi', 'SMO165G0033' => 'smo', 'SMO329G0094' => 'smo', 'SMO361G0276' => 'smo', 'Solyc01g006050.2' => 'sly', 'Solyc01g017600.3' => 'sly', 'Solyc04g014520.1' => 'sly', 'Solyc08g075970.3' => 'sly', 'Solyc10g050430.1' => 'sly', 'Sopen01g002050' => 'spe', 'Sopen01g013430' => 'spe', 'Sopen01g013830' => 'spe', 'Sopen08g024620' => 'spe', 'Sopen10g022080' => 'spe', 'Sp1g27790' => 'spa', 'Sp1g36300' => 'spa', 'Sp6g24520' => 'spa', 'TAR369G0751' => 'tar', 'TAR375G0488' => 'tar', 'TAR623G0463' => 'tar', 'TAR623G0569' => 'tar', 'THA.LOC104808456' => 'tha', 'THA.LOC104810352' => 'tha', 'THA.LOC104812763' => 'tha', 'THA.LOC104822627' => 'tha', 'Thecc.02G028400' => 'tca', 'Thecc.03G315500' => 'tca', 'Thecc.09G213900' => 'tca', 'Thhalv10008495m.g' => 'esa', 'Thhalv10011694m.g' => 'esa', 'Thhalv10011951m.g' => 'esa', 'Thhalv10012138m.g' => 'esa', 'Thhalv10012170m.g' => 'esa', 'Thhalv10014218m.g' => 'esa', 'Thhalv10023007m.g' => 'esa', 'TPR.G10223' => 'tpr', 'TPR.G14180' => 'tpr', 'TPR.G14191' => 'tpr', 'TPR.G14197' => 'tpr', 'TPR.G2455' => 'tpr', 'TPR.G2462' => 'tpr', 'TPR.G31321' => 'tpr', 'TWI34G0473' => 'twi', 'TWI60G0004' => 'twi', 'TWI60G0171' => 'twi', 'TWI60G0230' => 'twi', 'TWI60G0923' => 'twi', 'TWI60G1642' => 'twi', 'TWI60G1693' => 'twi', 'TWI75G0428' => 'twi', 'TWI79G0515' => 'twi', 'unitig_0.g2216' => 'ugi', 'unitig_749.g14104' => 'ugi', 'vmacro00071' => 'vma', 'vmacro02159' => 'vma', 'vmacro14226' => 'vma', 'VMungo0251G1403' => 'vmu', 'VMungo0331G0765' => 'vmu', 'VMungo0540G0397' => 'vmu', 'VMungo0720G2357' => 'vmu', 'VMungo1215G0728' => 'vmu', 'VMungo1215G0730' => 'vmu', 'Zm00001eb165180' => 'zma', 'Zm00001eb166570' => 'zma', 'Zm00001eb167000' => 'zma', 'Zm00001eb263140' => 'zma', 'Zm00001eb276230' => 'zma', 'Zm00001eb314320' => 'zma', 'Zm00001eb314330' => 'zma' ) $gf_id = 'HOM05D001193' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001193' ) $data_identifier = 'HOM05D001193' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 5, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 8, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'sun' => (int) 1, 'lal' => (int) 6, 'lja' => (int) 7, 'lonja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 9, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 8, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 17, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 7, 'twi' => (int) 9, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb314330' $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